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Touched upon in the internal meeting just now as well as at the end https://github.com/broadinstitute/lrma-aou1-panel-creation/issues/11#issuecomment-2253312774.
The goal is to understand represent…
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The use of HG002.1 and HG002.2 is confusing as the dot number is almost always used in genomics data to indicate a version number.
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Hi
I've encountered an issue when assembling the MHC region using individual HiFi data. I noticed that some sequences are assigned to both hap1 and hap2. For instance, hap1 assembled two different al…
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Hi,
I used HiFi + ONT + HiC reads to assemble haplotype genomes, then I want to classfiy hifi reads into haplotype genome separately.
I have tried to use minimap2, due to the similar haplotype g…
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Hi Emmanuel,
I am working with phased loci data in pegas - when I was trying to compute pairwise distances among haplotypes, using dist.haplotype.loci(), I came across the error:
"Error in Ops.f…
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I have a dataset of 1480 individuals that i want to visualize 2 ways (dividing into 19 groups corresponding to locality and 2 groups corresponding to species). I can load the TCS graph file and visual…
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This is the result of join_data.R for multi
chrom | pos | ref | alt | measureset_type | measureset_id | rcv | allele_id | symbol | hgvs_c | clinical_significance | clinical_significance_ordered | …
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The naive diploid Viterbi algorithm doesn't scale well with the number of reference haplotypes, slowing testing (#65). @astheeggeggs suggested an alternative implementation that "merges" partial ances…
szhan updated
5 months ago
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The `SegSiteStructure` objects (defined [here](https://github.com/DanielSeidman/MutationScripts/blob/be44de33dcebcafa04677a3f711e6911a98137dc/MutationCaller3.py#L160)) look like they're intended to ho…
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I’ve been noticing the following issues with radhaplotyper for a while and am finally getting around to asking about it. I’ve listed one example for each of several different undesirable decisions ma…